Update paraGRAPH filtering and adjust nimble report FileType

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/ParagraphStep.java

@@ -124,11 +124,7 @@ else if (!svVcf.exists())
                     SelectVariantsWrapper svw = new SelectVariantsWrapper(ctx.getLogger());
                     List<String> selectArgs = new ArrayList<>();
                     selectArgs.add("-select");
-                    selectArgs.add("SVTYPE != 'BND'");
-                    selectArgs.add("-select");
-                    selectArgs.add("!(vc.hasAttribute('SVTYPE') && vc.getAttribute('SVTYPE') == 'INS' && vc.hasSymbolicAlleles() && !vc.hasAttribute('SEQ'))");
-                    selectArgs.add("-select");
-                    selectArgs.add("POS > 150");
+                    selectArgs.add("SVTYPE != 'BND' && POS > 150 && !(vc.hasAttribute('SVTYPE') && vc.getAttribute('SVTYPE') == 'INS' && vc.hasSymbolicAlleles() && !vc.hasAttribute('SEQ'))");
                     selectArgs.add("--exclude-filtered");
                     selectArgs.add("--exclude-filtered");
                     selectArgs.add("--sites-only-vcf-output");

singlecell/src/org/labkey/singlecell/run/RepeatNimbleReportHandler.java

@@ -52,12 +52,12 @@ public RepeatNimbleReportHandler()
         );
     }
 
-    private static final FileType _nimbleResultsGz = new FileType(".txt.gz", FileType.gzSupportLevel.NO_GZ);
+    private static final FileType _nimbleResultsGz = new FileType(".txt", FileType.gzSupportLevel.SUPPORT_GZ);
 
     @Override
     public boolean canProcess(SequenceOutputFile o)
     {
-        return o.getFile() != null && o.getFile().exists() && o.getFile().getName().startsWith("reportResults") && _nimbleResultsGz.isType(o.getFile());
+        return o.getFile() != null && o.getFile().exists() && o.getFile().getName().startsWith("reportResults.") && _nimbleResultsGz.isType(o.getFile());
     }
 
     @Override